Biology subjects

Moran, S.

Publications and source records attributed to Moran, S..

10 recordsLinked to original sources

bioRxiv2026

Vocal Tract Disparity and Potential Implications for Speaker Recognition

Perceptual experiments show that listeners recognize female speakers with lower accuracy than male speakers. Automatic speaker recognition systems may also show performance bias against female speakers even when training data sets are gender balanced. The underlying reasons for this discrepancy are unclear. Here, we apply geometric morphometrics to quantify sex-related morphological vocal tract disparity -- the extent of shape variation -- across both resting and articulatory configurations. We find that male speakers exhibit greater disparity in both resting and articulatory configurations. This morphological idiosyncrasy may in turn generate more discriminable acoustic signatures and offer a biological explanation for higher recognition accuracies for male voices by humans and machines. Our results suggest that innate variation in vocal tract morphology may contribute to performance bias in voice technology and voice perception by human listeners.

evolutionary biology↗

bioRxiv2025

Pan-cancer 3D genomic analysis revealed extremely long Polycomb loops as the biomarker for sensitivity to Polycomb inhibition

Polycomb targeted loci form long-range chromatin interactions independent of CTCF-cohesion and are demarcated by low DNA methylation(1-3). Polycomb targets form extremely long-range loops (long Polycomb loops) that can separate anchors up to 60 Mb. These loops predominantly occur in cells of self-renewal status, such as human hematopoietic stem cells (HSC) and mouse embryonic stem cells (ESC), but rarely in cell lines. To identify long Polycomb loops in cancer, we initiated a pan-cancer survey of long Polycomb loops in a collection of 264 tumor samples (33 acute myeloid leukemias, 17 T cell lymphoblastic leukemia, 29 Breast cancer samples, 63 pediatric brain tumors, 70 prostate cancers, and 42 colon cancers). We found most cancers, including all prostate cancers and colon cancers, lack long Polycomb loops except pediatric brain tumors and certain AMLs. In pediatric brain tumors, we found 30% of the ependymoma PFA subtype (which shows globally depleted H3K27me3) notably displayed strong long Polycomb loop interactions. AML displayed more diverse levels of long Polycomb loop interactions. Most AMLs lost both long Polycomb loops with Polycomb binding loss at the loop anchors. Whereas 10% of AMLs retain long Polycomb loops as strong as in HSCs. These AMLs recurrently carry mutations in CEBPA and STAG2, which are not associated with the Polycomb complex or DNA methylation machinery. We found that long Polycomb loop strong AML is sensitive to EZH2 inhibition, which induces cell differentiation. Conversely, PRC1 component dependency can be used to predict long Polycomb loop formation in B-cell lymphoblastic leukemia cell lines. Our analysis suggests that the oncogenesis process antagonizes the long Polycomb loop maintenance in most cancers, yet certain cancers may still preserve strong long Polycomb loops from cell-of-origin. The maintenance of long Polycomb loops sensitizes cells to Polycomb inhibition, indicating that such loops could be an epigenomic biomarker for pharmacological or genetic Polycomb inhibition.

cancer biology↗

bioRxiv2025

Rule-based sequences in sooty mangabey vocal communication

Investigating how non-human animals produce call sequences provides key insights into the evolutionary origins of meaning in vocal communication, including syntax. Many species combine calls into structured sequences, often following specific rules, yet most studies focus on only a few sequences per species. This limits our understanding of their ability to combine calls and convey meaning through sequences. Our study addresses this gap by documenting the vocal sequence repertoire and underlying rules of sooty mangabeys (Cercocebus atys), a West African monkey species. We collected and analysed 1,672 recordings from two wild groups in the Tai National Park, Ivory Coast. Sooty mangabeys frequently combine calls but rely on a limited set of sequences. Within these, we identified rules of call ordering, recurrence and hierarchical structuring. Notably, they produced hierarchically structured sequences using only two call types, a previously unreported system in animal communication. Our findings suggest that sooty mangabeys use both structured and unstructured sequences, likely encoding different types of information. While context of production remains essential for determining meaning, our results highlight how a whole-repertoire approach reveals the full range of rule-based sequences and their potential for meaning expansion beyond the number of individual calls available in the repertoire.

animal behavior and cognition↗

bioRxiv2024

The SWI/SNF PBAF complex facilitates REST occupancy at repressive chromatin

Multimeric SWI/SNF chromatin remodelers assemble into discrete conformations with unique complex functionalities difficult to dissect. Distinct cancers harbor mutations in specific subunits, altering the chromatin landscape, such as the PBAF-specific component ARID2 in melanoma. Here, we performed comprehensive epigenomic profiling of SWI/SNF complexes and their associated chromatin states in melanoma and melanocytes and uncovered a subset of PBAF-exclusive regions that coexist with PRC2 and repressive chromatin. Time-resolved approaches revealed that PBAF regions are generally less sensitive to ATPase-mediated remodeling than BAF sites. Moreover, PBAF/PRC2-bound loci are enriched for REST, a transcription factor that represses neuronal genes. In turn, absence of ARID2 and consequent PBAF complex disruption hinders the ability of REST to bind and inactivate its targets, leading to upregulation of synaptic transcripts. Remarkably, this gene signature is conserved in melanoma patients with ARID2 mutations. In sum, we demonstrate a unique role for PBAF in generating accessibility for a silencing transcription factor at repressed chromatin, with important implications for disease.

molecular biology↗

bioRxiv2024

Interindividual vocal tract diversity influences the phonetic diversification of spoken languages

Vocal tracts, like other physical traits, exhibit extensive interindividual variation. However, little is known about how this variation translates into phonetic diversity between speakers, and ultimately, across languages. We demonstrate that different vocal tract shapes and associated articulatory strategies leave consistent acoustic signatures, which show congruent patterns of phonetic variation both within and across speech communities. Recalling a central tenet of evolutionary biology - that within-group variation feeds processes of between-group diversification - our findings suggest that the sounds of language evolve according to a neutral-like evolutionary process. Our "neutral-like evolution model" serves as a null hypothesis for disentangling the biological versus cultural mechanisms at play in phonetic diversification, where deviations from the neutral expectation indicate culturally mediated processes of language change at work.

evolutionary biology↗

bioRxiv2024

HERV-derived epitopes represent new targets for T-cell based immunotherapies in ovarian cancer

BackgroundOvarian cancer represents the most lethal gynecological cancer with poor results of checkpoint inhibitors. Human endogenous retroviruses (HERVs) are aberrantly expressed by tumor cells and may represent a source of shared T cell epitopes for cancer immunotherapy regardless of the tumor mutational burden. MethodsA transcriptomic analysis based on RNA-sequencing (RNA-seq) was developed to quantify the expression of HERV-K sequences containing the selected epitopes. The presence of HERV-K/HML-2 Gag antigen was then assessed by immunohistochemistry (IHC) on tumor microarrays from ovarian cancer samples and normal ovarian tissues. A specific immunopeptidomics approach was developed to detect epitopes on HLA molecules. Epitope-specific CD8+ T cells were quantified by multimer staining and in vitro target cell killing was evaluated using xCELLigence technology. In vivo antitumor efficacy of HERV-specific T cells was assessed in an avian embryo model. ResultsEpitope-containing HERV transcripts were significantly higher in ovarian cancers compared to normal tissues. The presence of HERV-K/HML-2 Gag antigen was confirmed by IHC in 20/40 (50%) ovarian cancers while no Gag expression was found in normal ovarian tissue samples. Immunopeptidomics analysis showed the presence of epitopes on HLA molecules on the surface of ovarian tumor cell lines but not on normal primary cells from critical tissues. HERV-specific T cells were detected among tumor infiltrating lymphocytes (TILs) from ovarian cancers, confirming the immunogenicity of these epitopes in patients. In vitro, HERV-specific T cells specifically killed ovarian cancer cells in an HLA class I-restricted manner while sparing normal HLA-A2-positive primary cells derived from critical tissues. Epitope-specific CD8+ T cells exhibited a strong anti-tumoral activity in vivo, inducing a highly significant decrease in tumor volume in comparison with control groups. ConclusionThese results provide the preclinical rationale for developing T-cell based approaches against HERV-K-derived epitopes in ovarian cancer. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=66 SRC="FIGDIR/small/603392v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@1c889b8org.highwire.dtl.DTLVardef@c9b0c5org.highwire.dtl.DTLVardef@1748100org.highwire.dtl.DTLVardef@1c129cc_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LISome HERVs are specifically overexpressed in ovarian cancer compared to normal tissues. C_LIO_LIHERV-K/HML-2 Gag antigen is detected by immunohistochemistry in ovarian cancers but not in normal ovarian tissues. Furthermore, HERV-K-derived epitopes are presented on HLA molecules on the surface of ovarian cancer cells but not on normal cells. C_LIO_LIThese epitopes are immunogenic in patients and induce high-avidity CD8+ T cells that specifically kill ovarian cancer cells in vitro and in vivo while sparing normal cells. C_LI

immunology↗

bioRxiv2021

Engineered ACE2-Fc counters murine lethal SARS-CoV-2 infection through direct neutralization and Fc-effector activities

Soluble Angiotensin-Converting Enzyme 2 (ACE2) constitutes an attractive antiviral capable of targeting a wide range of coronaviruses utilizing ACE2 as their receptor. Here, using structure-guided approaches, we developed divalent ACE2 molecules by grafting the extracellular ACE2-domain onto a human IgG1 or IgG3 (ACE2-Fc). These ACE2-Fcs harbor structurally validated mutations that enhance spike (S) binding and remove angiotensin enzymatic activity. The lead variant bound tightly to S, mediated in vitro neutralization of SARS-CoV-2 variants of concern (VOCs) with sub-nanomolar IC50 and was capable of robust Fc-effector functions, including antibody-dependent-cellular cytotoxicity, phagocytosis and complement deposition. When tested in a stringent K18-hACE2 mouse model, it delayed death or effectively resolved lethal SARS-CoV-2 infection in a prophylactic or therapeutic setting utilizing the combined effect of neutralization and Fc-effector functions. These data confirm the utility of ACE2-Fcs as valuable agents in preventing and eliminating SARS-CoV-2 infection and demonstrate that ACE2-Fc therapeutic activity require Fc-effector functions.

microbiology↗

bioRxiv2020

Languages, evolution and statistics: human sound systems were shaped by changes in bite configuration. Response to Tarasov & Uyeda (2020)

In Blasi et al. (2019) we have shown, through a series of statistical analyses and models, that human sound systems have been affected by a transition in bite configuration starting from the Neolithic. Tarasov and Uyeda (2020) (henceforth T&U) raise a number of observations in relation to our article. We appreciate T&Us engagement with our work and their sharing of the code and data of the analyses reported. In brief, their technical comment involves five analyses: O_LIBinomial Causal Models (BCM) C_LIO_LILinear Regression of across-area variation in labiodentals and subsistence C_LIO_LIPredictive Posterior Simulations (PPS) C_LIO_LIPoisson Linear Regression (PLR): model comparison C_LIO_LIPhylogenetic Analyses C_LI In what follows, we show that the discrepancies they report between our findings and theirs are due mostly to ill-specified models, weak (or missing) statistical evidence, and a misinterpretation of our results. After these issues are addressed, we conclude that T&Us claims do not hold.

evolutionary biology↗

bioRxiv2019

Identification of 20 novel loci associated to ischemic stroke. Epigenome-Wide Association Study

RationaleDNA methylation is dynamic, varies throughout the life course, and its levels are influenced by lifestyle and environmental factors, as well as by genetic variation. The leading genetic variants at stroke risk loci identified to date explain roughly 1-2% of stroke heritability. Most of these single nucleotide polymorphisms are situated within a regulatory sequence marked by DNase I hypersensitivity sites, which would indicate involvement of an epigenetic mechanism. ObjectiveTo detect epigenetic variants associated to stroke occurrence and stroke subtypes. Methods and ResultsA two-stage case-control epigenome-wide association study was designed. The discovery sample with 401 samples included 218 ischemic stroke (IS) patients, assessed at Hospital del Mar (Barcelona, Spain) and 183 controls from the REGICOR cohort. In two independent samples (N=226 and N=166), we replicated 22 CpG sites differentially methylated in IS in 21 loci, including 2 CpGs in locus ZFHX3, which includes known genetic variants associated with stroke. The pathways associated to these loci are inflammation and angiogenesis. The meta-analysis identified 384 differentially methylated CpGs, including loci of known stroke and vascular risk genetic variants, enriched by loci involved in lipid metabolism, adipogenesis, circadian clock, and glycolysis pathways. Stratification analysis by stroke subtypes revealed distinct methylation patterns. ConclusionsWe identified a set of 22 CpGs in 21 loci associated with IS. Our analysis suggests that DNA methylation changes may contribute to orchestrating gene expression that contributes to IS.

genetics↗

bioRxiv2017

An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures

Anaplastic meningioma is a rare and aggressive brain tumor characterised by intractable recurrences and dismal outcomes. Here, we present an integrated analysis of the whole genome, transcriptome and methylation profiles of primary and recurrent anaplastic meningioma. A key finding was the delineation of two distinct molecular subgroups that were associated with diametrically opposed survival outcomes. Relative to lower grade meningiomas, anaplastic tumors harbored frequent driver mutations in SWI/SNF complex genes, which were confined to the poor prognosis subgroup. Our analyses discern two biologically distinct variants of anaplastic meningioma with potential prognostic and therapeutic significance.

genomics↗